Low salt Vs Control
jeff karnsomprot
2025-06-29
1 Loading in Data sets + Library packages.
##
## The downloaded binary packages are in
## /var/folders/7n/x74qctp91rng390gx0z9hmd80000gn/T//RtmpmqpUvw/downloaded_packages2 Loading Dataset
options(future.globals.maxSize = 74 * 1024^3) # 55 GB
getOption("future.globals.maxSize") #59055800320## [1] 79456894976Idents(SO4) <- "subclass2_MD"
SO4$sample <- factor(SO4$sample, levels = c("SO1", "SO4", "SO3", "SO2"))
VlnPlot(SO4,"S100g",split.by = "treatment",group.by = "sample")## The default behaviour of split.by has changed.
## Separate violin plots are now plotted side-by-side.
## To restore the old behaviour of a single split violin,
## set split.plot = TRUE.
##
## This message will be shown once per session.## Warning: The `slot` argument of `FetchData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning: `PackageCheck()` was deprecated in SeuratObject 5.0.0.
## ℹ Please use `rlang::check_installed()` instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
# Macula Densa Markers , Nos1, Avpr1a, Slc12a1, Ptgs2, and Slc9a2
VlnPlot(SO4, c("Nos1","Avpr1a","Slc12a1","Ptgs2","Slc9a2","Pappa2"),split.by = "treatment",group.by = "treatment")
## Warning: The following arguments are not used: drop
3 Markers of control vs low_salt up/down regulation
Upregulated = low salt, positive, activated by low_salt Downregulated = control, negative, supressed of low_salt
Idents(SO4) <- "treatment"
type_markers <- FindMarkers(
object = SO4,
ident.1 = "low_salt",
ident.2 = "control",
group.by = "treatment",
min.pct = 0.1,
logfc.threshold = 0.1,
only.pos = FALSE
)## Warning: The `slot` argument of `GetAssayData()` is deprecated as of SeuratObject 5.0.0.
## ℹ Please use the `layer` argument instead.
## ℹ The deprecated feature was likely used in the Seurat package.
## Please report the issue at <https://github.com/satijalab/seurat/issues>.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## For a (much!) faster implementation of the Wilcoxon Rank Sum Test,
## (default method for FindMarkers) please install the presto package
## --------------------------------------------
## install.packages('devtools')
## devtools::install_github('immunogenomics/presto')
## --------------------------------------------
## After installation of presto, Seurat will automatically use the more
## efficient implementation (no further action necessary).
## This message will be shown once per session type_markers$gene <- rownames(type_markers)
type_markers <-type_markers %>% arrange(desc(avg_log2FC))3.1 Pathway Upregulated = Low salt
df<- type_markers
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers1up <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 3.19% of input gene IDs are fail to map...markers1up <- ENTREZ_list %>% inner_join(markers1up, by = "SYMBOL")
markers1up <- markers1up %>% dplyr::filter(p_val_adj < 0.05)
#head(markers, n = 50)
pos.markers1up <- markers1up %>% dplyr::filter(avg_log2FC > 0.3) %>% arrange(desc(abs(avg_log2FC)))
#change around avg log value
pos.ranks1up <- pos.markers1up$ENTREZID[abs(pos.markers1up$avg_log2FC) > 0]
#head(pos.ranks)
pos_go1up <- enrichGO(gene = pos.ranks1up, #a vector of entrez gene id
OrgDb = "org.Mm.eg.db",
ont = "BP",
readable = TRUE) #whether mapping gene ID to gene Name
pos_go1up## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:196] "239435" "16010" "19283" "23850" "19225" "66815" "70337" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...260 enriched terms found
## 'data.frame': 260 obs. of 12 variables:
## $ ID : chr "GO:0061077" "GO:0007179" "GO:0010563" "GO:0045936" ...
## $ Description : chr "chaperone-mediated protein folding" "transforming growth factor beta receptor signaling pathway" "negative regulation of phosphorus metabolic process" "negative regulation of phosphate metabolic process" ...
## $ GeneRatio : chr "8/189" "11/189" "14/189" "14/189" ...
## $ BgRatio : chr "69/28928" "218/28928" "388/28928" "388/28928" ...
## $ RichFactor : num 0.1159 0.0505 0.0361 0.0361 0.0427 ...
## $ FoldEnrichment: num 17.75 7.72 5.52 5.52 6.54 ...
## $ zScore : num 11.29 8.08 7.27 7.27 7.56 ...
## $ pvalue : num 1.70e-08 2.19e-07 3.01e-07 3.01e-07 3.69e-07 ...
## $ p.adjust : num 5.17e-05 2.08e-04 2.08e-04 2.08e-04 2.08e-04 ...
## $ qvalue : num 3.95e-05 1.59e-04 1.59e-04 1.59e-04 1.59e-04 ...
## $ geneID : chr "Hspb1/Hspa1a/Hspa1b/Hspa8/Hspa5/Clu/Fkbp5/Dnajb1" "Fos/Cav2/Cdkn1c/Bmp2/Bambi/Spry1/Jun/Hspa5/Cited1/Fut8/Tsc22d1" "Hspb1/Dusp1/Cdkn1c/Bmp2/Aldob/Rgs2/Cdk5rap1/Spry1/Ier3/Jun/Sh3bp5/Gstp1/Dynll1/Irf1" "Hspb1/Dusp1/Cdkn1c/Bmp2/Aldob/Rgs2/Cdk5rap1/Spry1/Ier3/Jun/Sh3bp5/Gstp1/Dynll1/Irf1" ...
## $ Count : int 8 11 14 14 12 5 12 13 10 12 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722 chart1up <- dotplot(pos_go1up) +
ggtitle("upregulated lowsalt") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)) +
scale_y_discrete(position = "right",
labels = function(x) str_wrap(x, width = 25)) # Wrap y-axis labels to 2 lines## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
### Upregulation Gene View
pathway_type1up <- strsplit(pos_go1up$geneID, "/")
names(pathway_type1up) <- pos_go1up$Description
pathway_type1up## $`chaperone-mediated protein folding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Hspa8" "Hspa5" "Clu" "Fkbp5" "Dnajb1"
##
## $`transforming growth factor beta receptor signaling pathway`
## [1] "Fos" "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Spry1" "Jun"
## [8] "Hspa5" "Cited1" "Fut8" "Tsc22d1"
##
## $`negative regulation of phosphorus metabolic process`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Bmp2" "Aldob" "Rgs2"
## [7] "Cdk5rap1" "Spry1" "Ier3" "Jun" "Sh3bp5" "Gstp1"
## [13] "Dynll1" "Irf1"
##
## $`negative regulation of phosphate metabolic process`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Bmp2" "Aldob" "Rgs2"
## [7] "Cdk5rap1" "Spry1" "Ier3" "Jun" "Sh3bp5" "Gstp1"
## [13] "Dynll1" "Irf1"
##
## $`cellular response to transforming growth factor beta stimulus`
## [1] "Fos" "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Wnt10a" "Spry1"
## [8] "Jun" "Hspa5" "Cited1" "Fut8" "Tsc22d1"
##
## $`protein refolding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Hspa8" "Hspa5"
##
## $`response to transforming growth factor beta`
## [1] "Fos" "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Wnt10a" "Spry1"
## [8] "Jun" "Hspa5" "Cited1" "Fut8" "Tsc22d1"
##
## $`transforming growth factor beta receptor superfamily signaling pathway`
## [1] "Fos" "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Spry1" "Hfe"
## [8] "Bmper" "Jun" "Hspa5" "Cited1" "Fut8" "Tsc22d1"
##
## $`negative regulation of transferase activity`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2" "Cdk5rap1"
## [7] "Spry1" "Zfp36" "Sh3bp5" "Gstp1"
##
## $`negative regulation of cell adhesion`
## [1] "Ptprz1" "Hspb1" "Dusp1" "Bcl6" "Bmp2" "Hfe" "Arg2" "Gstp1"
## [9] "Irf1" "Acer2" "Pik3r1" "Adam15"
##
## $`chaperone cofactor-dependent protein refolding`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Hspa5" "Dnajb1"
##
## $`negative regulation of phosphorylation`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2" "Cdk5rap1"
## [7] "Spry1" "Jun" "Sh3bp5" "Gstp1" "Dynll1" "Irf1"
##
## $`negative regulation of protein kinase activity`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2" "Cdk5rap1" "Spry1"
## [8] "Sh3bp5" "Gstp1"
##
## $`cell surface receptor protein serine/threonine kinase signaling pathway`
## [1] "Fos" "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Spry1" "Hfe"
## [8] "Bmper" "Jun" "Hspa5" "Cited1" "Fut8" "Tsc22d1"
##
## $`response to heat`
## [1] "Ptgs2" "Hspb1" "Hspa1a" "Hspa1b" "Hspa8" "Nos1" "Dnajb1"
##
## $`negative regulation of protein modification process`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2" "Cdk5rap1"
## [7] "Hspa1b" "Spry1" "Jun" "Sh3bp5" "Bex2" "Gstp1"
## [13] "Irf1"
##
## $`negative regulation of kinase activity`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2" "Cdk5rap1" "Spry1"
## [8] "Sh3bp5" "Gstp1"
##
## $`negative regulation of protein phosphorylation`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Bmp2" "Rgs2" "Cdk5rap1"
## [7] "Spry1" "Jun" "Sh3bp5" "Gstp1" "Irf1"
##
## $`response to metal ion`
## [1] "Ptgs2" "Fos" "Junb" "Chp2" "Aldob" "Hfe" "Hspa8"
## [8] "Jun" "Trpc1" "Pla2g4a" "Slc41a1" "Kcnc2"
##
## $`regulation of inclusion body assembly`
## [1] "Hspa1b" "Hap1" "Clu" "Dnajb1"
##
## $`ureteric bud development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2" "Hoxb7"
##
## $`'de novo' post-translational protein folding`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Hspa5" "Dnajb1"
##
## $`mesonephric epithelium development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2" "Hoxb7"
##
## $`mesonephric tubule development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2" "Hoxb7"
##
## $`'de novo' protein folding`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Hspa5" "Dnajb1"
##
## $`mesonephros development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2" "Hoxb7"
##
## $`positive regulation of cell projection organization`
## [1] "Ptprz1" "Ache" "Hspb1" "Rgs2" "Scarf1" "Lcn2" "Hap1"
## [8] "Dynlt1f" "Dynll1" "Hspa5" "Robo2" "Cx3cl1" "Pik3r1"
##
## $`negative regulation of neuron apoptotic process`
## [1] "Ptprz1" "Btg2" "Lcn2" "Jun" "Cited1" "Tox3" "Clu" "Cx3cl1"
## [9] "Nos1"
##
## $`kidney epithelium development`
## [1] "Bmp2" "Spry1" "Bmper" "Arg2" "Cited1" "Robo2" "Hoxb7" "Irx1"
##
## $`calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules`
## [1] "Bmp2" "Cldn4" "Cx3cl1" "Cldn3"
##
## $`response to temperature stimulus`
## [1] "Ptgs2" "Hspb1" "Hspa1a" "Hspa1b" "Hspa8" "Rbm3" "Nos1" "Dnajb1"
##
## $`regulation of epithelial cell differentiation`
## [1] "Cdkn1c" "Sfn" "Etv4" "Bmp2" "F11r" "Spry1" "Zfp36" "Cited1"
##
## $`negative regulation of MAP kinase activity`
## [1] "Dusp1" "Bmp2" "Rgs2" "Spry1" "Gstp1"
##
## $regeneration
## [1] "Mcub" "Mymx" "Scarf1" "Hfe" "Cspg5" "Jun" "Gstp1" "Cpq"
## [9] "Adam15"
##
## $`protein folding`
## [1] "Hspb1" "Hspa1a" "Hspa1b" "Hspa8" "Hspa5" "Clu" "Fkbp5" "Dnajb1"
##
## $`response to phorbol 13-acetate 12-myristate`
## [1] "Fos" "Btg2" "Adam15"
##
## $`cellular response to phorbol 13-acetate 12-myristate`
## [1] "Fos" "Btg2" "Adam15"
##
## $`osteoclast differentiation`
## [1] "Fos" "Junb" "Bmp2" "Klf10" "Anxa2" "Mafb" "Pik3r1"
##
## $`response to topologically incorrect protein`
## [1] "Hspb1" "Hspa1a" "Manf" "Hspa5" "Clu" "Serp2" "Pik3r1"
##
## $`SMAD protein signal transduction`
## [1] "Fos" "Bmp2" "Hfe" "Bmper" "Jun" "Cited1"
##
## $`negative regulation of protein serine/threonine kinase activity`
## [1] "Dusp1" "Bmp2" "Rgs2" "Cdk5rap1" "Spry1" "Gstp1"
##
## $`kidney development`
## [1] "Cdkn1c" "Bmp2" "Spry1" "Hspa8" "Bmper" "Arg2" "Cited1" "Robo2"
## [9] "Id3" "Hoxb7" "Irx1"
##
## $`prostaglandin transport`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Slco4a1"
##
## $`inclusion body assembly`
## [1] "Hspa1b" "Hap1" "Clu" "Dnajb1"
##
## $`regulation of hemopoiesis`
## [1] "Fos" "Hspb1" "Bcl6" "Cd83" "Hspa1b" "Klf10" "Zfp36"
## [8] "Jun" "Irf1" "Mafb" "Pik3r1" "Tsc22d1"
##
## $`regulation of transforming growth factor beta receptor signaling pathway`
## [1] "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Spry1" "Hspa5" "Tsc22d1"
##
## $`renal system development`
## [1] "Cdkn1c" "Bmp2" "Spry1" "Hspa8" "Bmper" "Arg2" "Cited1" "Robo2"
## [9] "Id3" "Hoxb7" "Irx1"
##
## $`negative regulation of cell-substrate adhesion`
## [1] "Ptprz1" "Bcl6" "Acer2" "Pik3r1" "Adam15"
##
## $`cellular response to metal ion`
## [1] "Ptgs2" "Fos" "Junb" "Chp2" "Hfe" "Hspa8" "Jun"
## [8] "Slc41a1"
##
## $`regulation of cellular response to transforming growth factor beta stimulus`
## [1] "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Spry1" "Hspa5" "Tsc22d1"
##
## $`prostaglandin metabolic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Gstp1" "Gstm1"
##
## $`prostanoid metabolic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Gstp1" "Gstm1"
##
## $`regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Spry1" "Hfe" "Bmper"
## [8] "Hspa5" "Tsc22d1"
##
## $`regulation of iron ion transport`
## [1] "Lcn2" "Hfe" "Nos1"
##
## $`negative regulation of cell-matrix adhesion`
## [1] "Bcl6" "Acer2" "Pik3r1" "Adam15"
##
## $`negative regulation of cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "Bmp2" "Hfe" "Arg2" "Gstp1" "Irf1" "Pik3r1"
##
## $`negative regulation of type 2 immune response`
## [1] "Bcl6" "Arg2" "Irf1"
##
## $`response to steroid hormone`
## [1] "Ptgs2" "Fos" "Junb" "Hspa8" "Zfp36" "Jun" "Cldn4" "Gstp1"
## [9] "Pik3r1" "Por"
##
## $`response to unfolded protein`
## [1] "Hspb1" "Hspa1a" "Manf" "Hspa5" "Serp2" "Pik3r1"
##
## $`regulation of membrane permeability`
## [1] "F11r" "Hspa8" "Ier3" "Dynlt1f" "Cldn3"
##
## $`regulation of metal ion transport`
## [1] "Ptgs2" "Mcub" "Lcn2" "Hfe" "Hap1" "Trpc1"
## [7] "Cacna2d1" "Cx3cl1" "Smim6" "Nos1" "Kcnc2"
##
## $`regulation of vesicle fusion`
## [1] "Syt5" "Pla2g4a" "Rab3a" "Anxa2"
##
## $`positive regulation of neuron projection development`
## [1] "Ptprz1" "Hspb1" "Rgs2" "Scarf1" "Hap1" "Dynlt1f" "Hspa5"
## [8] "Cx3cl1"
##
## $`carboxylic acid transport`
## [1] "Ptgs2" "Ptges" "Rgs2" "Slc6a7" "Pla2g4a" "Arg2"
## [7] "Slco4a1" "Slc16a11" "Lrrc8c" "Kcnk1"
##
## $`organic acid transport`
## [1] "Ptgs2" "Ptges" "Rgs2" "Slc6a7" "Pla2g4a" "Arg2"
## [7] "Slco4a1" "Slc16a11" "Lrrc8c" "Kcnk1"
##
## $`negative regulation of hemopoiesis`
## [1] "Hspb1" "Bcl6" "Irf1" "Mafb" "Pik3r1" "Tsc22d1"
##
## $`response to alcohol`
## [1] "Fos" "Btg2" "Rgs2" "Hspa8" "Gstp1" "Pmvk" "Cldn3" "Fkbp5"
## [9] "Adam15" "Kcnc2"
##
## $`membrane fusion`
## [1] "Syt5" "Cav2" "Mymx" "Pla2g4a" "Rab3a" "Anxa2" "Stxbp6"
##
## $`amide metabolic process`
## [1] "Degs2" "Aldob" "Hap1" "Arg2" "Gstp1" "Acer2" "Clu" "Pmvk" "Gstm1"
## [10] "Cmas" "Gsta4"
##
## $`vesicle fusion`
## [1] "Syt5" "Cav2" "Pla2g4a" "Rab3a" "Anxa2" "Stxbp6"
##
## $`negative regulation of apoptotic signaling pathway`
## [1] "Ptgs2" "Hspb1" "Hspa1b" "Ier3" "Gstp1" "Clu" "Cx3cl1" "Pam16"
##
## $`organelle membrane fusion`
## [1] "Syt5" "Cav2" "Pla2g4a" "Rab3a" "Anxa2" "Stxbp6"
##
## $`nitric oxide biosynthetic process`
## [1] "Ptgs2" "Dynll1" "Clu" "Nos1" "Por"
##
## $`prostaglandin secretion`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`regulation of receptor binding`
## [1] "Hfe" "Anxa2" "Adam15"
##
## $`negative regulation of alpha-beta T cell activation`
## [1] "Bcl6" "Hfe" "Arg2" "Irf1"
##
## $`regulation of neuron apoptotic process`
## [1] "Ptprz1" "Btg2" "Lcn2" "Jun" "Cited1" "Tox3" "Clu" "Cx3cl1"
## [9] "Nos1"
##
## $`regulation of tumor necrosis factor production`
## [1] "Hspb1" "Zfp36" "Arg2" "Gstp1" "Clu" "Cx3cl1" "Pik3r1"
##
## $`regulation of tumor necrosis factor superfamily cytokine production`
## [1] "Hspb1" "Zfp36" "Arg2" "Gstp1" "Clu" "Cx3cl1" "Pik3r1"
##
## $`tumor necrosis factor production`
## [1] "Hspb1" "Zfp36" "Arg2" "Gstp1" "Clu" "Cx3cl1" "Pik3r1"
##
## $`regulation of monoatomic cation transmembrane transport`
## [1] "Mcub" "Lcn2" "Hap1" "Trpc1" "Cacna2d1" "Cx3cl1" "Smim6"
## [8] "Nos1" "Kcnc2"
##
## $`regulation of protein kinase activity`
## [1] "Hspb1" "Dusp1" "Cdkn1c" "Sfn" "Bmp2" "Rgs2"
## [7] "Cdk5rap1" "Spry1" "Sh3bp5" "Gstp1" "Map2k3"
##
## $`response to calcium ion`
## [1] "Fos" "Junb" "Chp2" "Jun" "Trpc1" "Pla2g4a"
##
## $`tumor necrosis factor superfamily cytokine production`
## [1] "Hspb1" "Zfp36" "Arg2" "Gstp1" "Clu" "Cx3cl1" "Pik3r1"
##
## $`nitric oxide metabolic process`
## [1] "Ptgs2" "Dynll1" "Clu" "Nos1" "Por"
##
## $`cellular response to chemical stress`
## [1] "Ptgs2" "Fos" "Hspb1" "Rhob" "Lcn2" "Hspa8" "Jun" "Fut8"
## [9] "Lrrc8c"
##
## $`cellular response to heat`
## [1] "Ptgs2" "Hspa1b" "Hspa8" "Dnajb1"
##
## $`negative regulation of transforming growth factor beta receptor signaling pathway`
## [1] "Cav2" "Bmp2" "Bambi" "Spry1" "Hspa5"
##
## $`reactive nitrogen species metabolic process`
## [1] "Ptgs2" "Dynll1" "Clu" "Nos1" "Por"
##
## $`negative regulation of response to external stimulus`
## [1] "Dusp1" "Sfn" "Zfp36" "Ier3" "Arg2" "Gstp1" "Anxa2" "Robo2"
## [9] "Cx3cl1" "Cldn3"
##
## $`regulation of acute inflammatory response`
## [1] "Ptgs2" "Ptges" "C2cd4b" "Gstp1"
##
## $`metanephros development`
## [1] "Spry1" "Cited1" "Robo2" "Id3" "Irx1"
##
## $`regulation of animal organ morphogenesis`
## [1] "Bmp2" "Wnt10a" "Spry1" "Robo2" "Hoxb7"
##
## $`negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cav2" "Bmp2" "Bambi" "Spry1" "Bmper" "Hspa5"
##
## $`sulfur compound biosynthetic process`
## [1] "B3gnt7" "Hs3st6" "Gstp1" "Ndst4" "Gstm1" "Mri1"
##
## $`organ induction`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`regulation of calcium ion transport`
## [1] "Ptgs2" "Mcub" "Hap1" "Trpc1" "Cacna2d1" "Cx3cl1" "Smim6"
## [8] "Nos1"
##
## $`negative regulation of leukocyte cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "Hfe" "Arg2" "Gstp1" "Irf1"
##
## $`p38MAPK cascade`
## [1] "Dusp1" "Bmp2" "Zfp36" "Map2k3"
##
## $`myeloid leukocyte differentiation`
## [1] "Fos" "Junb" "Bmp2" "Klf10" "Jun" "Anxa2" "Mafb" "Pik3r1"
##
## $`muscle cell proliferation`
## [1] "Ptgs2" "Fos" "Cav2" "Bmp2" "Jun" "Gstp1" "Cx3cl1" "Pik3r1"
##
## $`response to glucocorticoid`
## [1] "Ptgs2" "Fos" "Zfp36" "Gstp1" "Pik3r1" "Por"
##
## $`positive regulation of cation transmembrane transport`
## [1] "Lcn2" "Hap1" "Trpc1" "Cx3cl1" "Nos1" "Kcnc2"
##
## $`positive regulation of transmembrane receptor protein serine/threonine kinase signaling pathway`
## [1] "Cdkn1c" "Bmp2" "Hfe" "Bmper" "Tsc22d1"
##
## $`regulation of ATP-dependent activity`
## [1] "Aldob" "Mcm2" "Smim6" "Dnajb1"
##
## $`fatty acid biosynthetic process`
## [1] "Ptgs2" "Ptges" "Lipg" "Pla2g4a" "Gstp1" "Gstm1"
##
## $`regulation of blood pressure`
## [1] "Ptgs2" "F11r" "Ier3" "Manf" "Pik3r1" "Nos1" "Klk1b3"
##
## $`regulation of leukocyte differentiation`
## [1] "Fos" "Hspb1" "Bcl6" "Cd83" "Klf10" "Jun" "Irf1" "Mafb"
## [9] "Pik3r1"
##
## $`glycoprotein metabolic process`
## [1] "Bmp2" "B3gnt7" "Tmtc1" "Hs3st6" "Acer2" "Galnt3" "Ndst4"
## [8] "St3gal4" "Fut8"
##
## $`response to tumor necrosis factor`
## [1] "Ptgs2" "Fos" "Hspa1b" "Traf1" "Zfp36" "Irf1" "Cx3cl1"
##
## $`cell-cell adhesion via plasma-membrane adhesion molecules`
## [1] "Bmp2" "Scarf1" "Cldn4" "Pcdh1" "Robo2" "Cx3cl1" "Cldn3"
##
## $`regulation of monoatomic ion transmembrane transport`
## [1] "Mcub" "Lcn2" "Hap1" "Trpc1" "Cacna2d1" "Cx3cl1" "Smim6"
## [8] "Nos1" "Kcnc2"
##
## $`response to ethanol`
## [1] "Fos" "Rgs2" "Hspa8" "Gstp1" "Cldn3" "Kcnc2"
##
## $`female pregnancy`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Hfe" "Cldn4" "Pla2g4a"
##
## $`iron ion transport`
## [1] "Lcn2" "Hfe" "Fth1" "Nos1"
##
## $`cell-substrate adhesion`
## [1] "Ptprz1" "Frem1" "Bcl6" "Limch1" "Cspg5" "Acer2" "Anxa2" "Pik3r1"
## [9] "Adam15"
##
## $`positive regulation of vesicle fusion`
## [1] "Syt5" "Pla2g4a" "Anxa2"
##
## $`negative regulation of muscle contraction`
## [1] "Ptgs2" "Rgs2" "Arg2"
##
## $`response to toxic substance`
## [1] "Ptgs2" "Fos" "Ptges" "Lcn2" "Pon2" "Gstp1" "Kcnc2"
##
## $`regulation of epidermis development`
## [1] "Sfn" "Etv4" "Zfp36" "Nab2"
##
## $`positive regulation of endothelial cell migration`
## [1] "Ptgs2" "Hspb1" "Rhob" "Lcn2" "Map2k3"
##
## $`regulation of cell-substrate adhesion`
## [1] "Ptprz1" "Bcl6" "Limch1" "Cspg5" "Acer2" "Pik3r1" "Adam15"
##
## $`regulation of myeloid cell differentiation`
## [1] "Fos" "Hspa1b" "Klf10" "Zfp36" "Jun" "Mafb" "Pik3r1"
##
## $`macrophage activation`
## [1] "Mcub" "Jun" "Pla2g4a" "Clu" "Cx3cl1"
##
## $`cell-matrix adhesion`
## [1] "Frem1" "Bcl6" "Limch1" "Acer2" "Anxa2" "Pik3r1" "Adam15"
##
## $`maternal process involved in female pregnancy`
## [1] "Ptgs2" "Junb" "Rgs2" "Pla2g4a"
##
## $`osteoblast differentiation`
## [1] "Ache" "Junb" "Bmp2" "Bambi" "Tent5a" "Cited1" "Id3"
##
## $`glycoprotein biosynthetic process`
## [1] "B3gnt7" "Tmtc1" "Hs3st6" "Acer2" "Galnt3" "Ndst4" "St3gal4"
## [8] "Fut8"
##
## $`plasma membrane organization`
## [1] "Cav2" "Mymx" "Rab3a" "Anxa2" "Clu" "Mafb"
##
## $`response to starvation`
## [1] "Fos" "Hfe" "Klf10" "Hspa8" "Zfp36" "Jun" "Hspa5"
##
## $`prostaglandin biosynthetic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`regulation of animal organ formation`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`prostanoid biosynthetic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a"
##
## $`cellular response to cadmium ion`
## [1] "Fos" "Hspa8" "Jun"
##
## $`icosanoid transport`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Slco4a1"
##
## $`organic anion transport`
## [1] "Ptgs2" "Ptges" "Rgs2" "Slc6a7" "Pla2g4a" "Arg2"
## [7] "Slco4a1" "Slc16a11" "Lrrc8c" "Kcnk1"
##
## $`regulation of endothelial cell migration`
## [1] "Ptgs2" "Hspb1" "Rhob" "Lcn2" "Bmper" "Map2k3"
##
## $`positive regulation of monoatomic ion transmembrane transport`
## [1] "Lcn2" "Hap1" "Trpc1" "Cx3cl1" "Nos1" "Kcnc2"
##
## $`acute inflammatory response`
## [1] "Ptgs2" "Ptges" "Hfe" "C2cd4b" "Gstp1"
##
## $`positive regulation of fat cell differentiation`
## [1] "Ptgs2" "Bmp2" "Zfp36" "Vstm2a"
##
## $`neuron apoptotic process`
## [1] "Ptprz1" "Btg2" "Lcn2" "Jun" "Cited1" "Tox3" "Clu" "Cx3cl1"
## [9] "Nos1"
##
## $decidualization
## [1] "Ptgs2" "Junb" "Pla2g4a"
##
## $`cardiac epithelial to mesenchymal transition`
## [1] "Bmp2" "Spry1" "Adam15"
##
## $`response to corticosteroid`
## [1] "Ptgs2" "Fos" "Zfp36" "Gstp1" "Pik3r1" "Por"
##
## $`regulation of neurogenesis`
## [1] "Ptprz1" "Ache" "Btg2" "Bmp2" "Hap1" "Anxa2" "Robo2"
## [8] "Cx3cl1" "Rassf10" "Nos1"
##
## $`negative regulation of leukocyte differentiation`
## [1] "Hspb1" "Bcl6" "Irf1" "Mafb" "Pik3r1"
##
## $`regulation of type 2 immune response`
## [1] "Bcl6" "Arg2" "Irf1"
##
## $`regulation of supramolecular fiber organization`
## [1] "Hspa1a" "Hspa1b" "F11r" "Limch1" "Hspa8" "Clu" "Capg" "Cx3cl1"
## [9] "Pik3r1"
##
## $`regulation of alpha-beta T cell activation`
## [1] "Bcl6" "Cd83" "Hfe" "Arg2" "Irf1"
##
## $`regulation of fibroblast proliferation`
## [1] "Ptprz1" "Jun" "Gstp1" "Anxa2" "Fth1"
##
## $`positive regulation of lipid localization`
## [1] "Ptges" "Lipg" "Vstm2a" "Pla2g4a" "Anxa2"
##
## $`organelle fusion`
## [1] "Syt5" "Cav2" "Pla2g4a" "Rab3a" "Anxa2" "Stxbp6"
##
## $`negative regulation of calcium ion transport`
## [1] "Ptgs2" "Mcub" "Smim6" "Nos1"
##
## $`regulation of cellular response to growth factor stimulus`
## [1] "Cav2" "Cdkn1c" "Bmp2" "Bambi" "Spry1" "Bmper" "Hspa5"
## [8] "Tsc22d1"
##
## $`response to xenobiotic stimulus`
## [1] "Ptgs2" "Fos" "Lcn2" "Hspa8" "Jun" "Gstp1" "Acer2" "Gstm1" "Gsta4"
## [10] "Nos1"
##
## $`cellular response to oxidative stress`
## [1] "Fos" "Hspb1" "Rhob" "Lcn2" "Hspa8" "Jun" "Fut8"
##
## $`multi-organism reproductive process`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Hfe" "Cldn4" "Pla2g4a"
##
## $`positive regulation of protein binding`
## [1] "Bmp2" "Bambi" "Hfe" "Anxa2"
##
## $`positive regulation of nucleocytoplasmic transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Pik3r1"
##
## $`regulation of calcium ion transmembrane transport`
## [1] "Mcub" "Hap1" "Trpc1" "Cacna2d1" "Cx3cl1" "Smim6"
##
## $`regulation of cell-matrix adhesion`
## [1] "Bcl6" "Limch1" "Acer2" "Pik3r1" "Adam15"
##
## $`positive regulation of proteolysis`
## [1] "Hspa1a" "Hspa1b" "Hspa8" "Cldn4" "Acer2" "Anxa2" "Clu" "Cldn3"
##
## $`regulation of lens fiber cell differentiation`
## [1] "Cdkn1c" "Spry1"
##
## $`regulation of lipid localization`
## [1] "Ptges" "Lipg" "Vstm2a" "Pla2g4a" "Anxa2" "Ttc39b"
##
## $`multi-multicellular organism process`
## [1] "Ptgs2" "Fos" "Junb" "Rgs2" "Hfe" "Cldn4" "Pla2g4a"
##
## $`regulation of protein serine/threonine kinase activity`
## [1] "Dusp1" "Sfn" "Bmp2" "Rgs2" "Cdk5rap1" "Spry1" "Gstp1"
##
## $`positive regulation of response to wounding`
## [1] "Scarf1" "Cldn4" "Cldn3" "St3gal4"
##
## $`response to mechanical stimulus`
## [1] "Ptgs2" "Fos" "Btg2" "F11r" "Jun" "Irf1" "Nos1"
##
## $`skeletal system morphogenesis`
## [1] "Pappa2" "Frem1" "Hoxc4" "Hoxb2" "Hoxb7" "Por" "Nab2"
##
## $`hormone metabolic process`
## [1] "Iyd" "Bmp2" "Hfe" "Slco4a1" "Cpq" "Akr1b8" "Por"
##
## $`cellular modified amino acid metabolic process`
## [1] "Iyd" "Gstp1" "Slco4a1" "Cpq" "Gstm1" "Gsta4"
##
## $`regulation of smooth muscle cell proliferation`
## [1] "Ptgs2" "Bmp2" "Jun" "Gstp1" "Cx3cl1" "Pik3r1"
##
## $`phenol-containing compound metabolic process`
## [1] "Iyd" "Trpc1" "Slco4a1" "Cited1" "Cpq"
##
## $`regulation of nucleocytoplasmic transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Ier3" "Pik3r1"
##
## $`fat cell differentiation`
## [1] "Ptgs2" "Bmp2" "Rgs2" "Zfp36" "Vstm2a" "Psmb8" "Lrrc8c"
##
## $`positive regulation of phosphatase activity`
## [1] "Chp2" "Bmp2"
##
## $`regulation of microtubule nucleation`
## [1] "Hspa1a" "Hspa1b"
##
## $`regulation of fever generation`
## [1] "Ptgs2" "Ptges"
##
## $`nitric oxide-cGMP-mediated signaling`
## [1] "Nos1" "Kcnc2"
##
## $`negative regulation of erythrocyte differentiation`
## [1] "Zfp36" "Mafb"
##
## $`negative regulation of inclusion body assembly`
## [1] "Hspa1b" "Dnajb1"
##
## $`positive regulation of unsaturated fatty acid biosynthetic process`
## [1] "Ptgs2" "Pla2g4a"
##
## $`regulation of response to endoplasmic reticulum stress`
## [1] "Manf" "Hspa5" "Clu" "Pik3r1"
##
## $`thyroid hormone metabolic process`
## [1] "Iyd" "Slco4a1" "Cpq"
##
## $`response to interleukin-4`
## [1] "Mcm2" "Hspa5" "Cited1"
##
## $`negative regulation of CD4-positive, alpha-beta T cell activation`
## [1] "Bcl6" "Arg2" "Irf1"
##
## $`negative regulation of leukocyte activation`
## [1] "Hspb1" "Bcl6" "Hfe" "Arg2" "Irf1" "Cx3cl1"
##
## $`sulfur compound metabolic process`
## [1] "B3gnt7" "Hs3st6" "Gstp1" "Pmvk" "Ndst4" "Gstm1" "Gsta4" "Mri1"
##
## $`response to oxidative stress`
## [1] "Ptgs2" "Fos" "Hspb1" "Rhob" "Lcn2" "Hspa8" "Jun" "Gstp1" "Fut8"
##
## $`leukocyte cell-cell adhesion`
## [1] "Hspb1" "Bcl6" "Cd83" "F11r" "Hfe" "Arg2" "Gstp1"
## [8] "Irf1" "St3gal4"
##
## $`cellular response to calcium ion`
## [1] "Fos" "Junb" "Chp2" "Jun"
##
## $`specification of animal organ identity`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`developmental induction`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`positive regulation of SMAD protein signal transduction`
## [1] "Bmp2" "Hfe" "Bmper"
##
## $`positive regulation of animal organ morphogenesis`
## [1] "Bmp2" "Spry1" "Robo2"
##
## $`response to endoplasmic reticulum stress`
## [1] "Manf" "Jun" "Hspa5" "Clu" "Nrbf2" "Serp2" "Pik3r1"
##
## $`cellular response to tumor necrosis factor`
## [1] "Fos" "Hspa1b" "Traf1" "Zfp36" "Irf1" "Cx3cl1"
##
## $`negative regulation of T cell activation`
## [1] "Hspb1" "Bcl6" "Hfe" "Arg2" "Irf1"
##
## $`negative regulation of locomotion`
## [1] "Dusp1" "Rhob" "Limch1" "Gstp1" "Robo2" "Cx3cl1" "Cldn3" "Adam15"
##
## $`smooth muscle cell proliferation`
## [1] "Ptgs2" "Bmp2" "Jun" "Gstp1" "Cx3cl1" "Pik3r1"
##
## $`regulation of prostaglandin biosynthetic process`
## [1] "Ptgs2" "Pla2g4a"
##
## $`macrophage proliferation`
## [1] "Clu" "Cx3cl1"
##
## $`chaperone-mediated autophagy`
## [1] "Hspa8" "Clu"
##
## $`regulation of nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway`
## [1] "Hspa1b" "Slc15a2"
##
## $`negative regulation of receptor binding`
## [1] "Hfe" "Adam15"
##
## $`positive regulation of non-motile cilium assembly`
## [1] "Hap1" "Dynll1"
##
## $`regulation of CD4-positive, alpha-beta T cell activation`
## [1] "Bcl6" "Cd83" "Arg2" "Irf1"
##
## $`regulation of regulatory T cell differentiation`
## [1] "Hspb1" "Bcl6" "Irf1"
##
## $`regulation of apoptotic signaling pathway`
## [1] "Ptgs2" "Hspb1" "Hspa1b" "Traf1" "Ier3" "Gstp1" "Clu" "Cx3cl1"
## [9] "Pam16"
##
## $`import across plasma membrane`
## [1] "Rgs2" "Lcn2" "Slc6a7" "Arg2" "Lrrc8c" "Slc15a2"
##
## $`nephron tubule morphogenesis`
## [1] "Bmp2" "Cited1" "Hoxb7" "Irx1"
##
## $`nucleocytoplasmic transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Hspa8" "Ier3" "Cited1" "Pik3r1"
## [8] "Htatip2"
##
## $`nuclear transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Hspa8" "Ier3" "Cited1" "Pik3r1"
## [8] "Htatip2"
##
## $`response to progesterone`
## [1] "Fos" "Hspa8" "Cldn4"
##
## $`neuroinflammatory response`
## [1] "Ptgs2" "Jun" "Clu" "Cx3cl1"
##
## $regionalization
## [1] "Btg2" "Bmp2" "Spry1" "Robo2" "Mafb" "Hoxc4" "Hoxb2" "Hoxb7" "Irx1"
##
## $`tissue regeneration`
## [1] "Mcub" "Mymx" "Cpq" "Adam15"
##
## $`nephron epithelium morphogenesis`
## [1] "Bmp2" "Cited1" "Hoxb7" "Irx1"
##
## $`positive regulation of dephosphorylation`
## [1] "Chp2" "Bmp2"
##
## $`positive regulation of nuclear-transcribed mRNA poly(A) tail shortening`
## [1] "Btg2" "Zfp36"
##
## $`regulation of metallopeptidase activity`
## [1] "Cldn4" "Cldn3"
##
## $`maternal placenta development`
## [1] "Ptgs2" "Junb" "Pla2g4a"
##
## $`negative regulation of chemotaxis`
## [1] "Dusp1" "Gstp1" "Robo2"
##
## $`positive regulation of release of sequestered calcium ion into cytosol`
## [1] "Hap1" "Trpc1" "Cx3cl1"
##
## $`alcohol metabolic process`
## [1] "Bmp2" "Degs2" "Pla2g4a" "Acer2" "Ttc39b" "Pmvk" "Akr1b8"
## [8] "Por"
##
## $`regulation of osteoclast differentiation`
## [1] "Fos" "Klf10" "Mafb" "Pik3r1"
##
## $`axo-dendritic transport`
## [1] "Hspb1" "Hspa8" "Hap1" "Rab17"
##
## $`nephron morphogenesis`
## [1] "Bmp2" "Cited1" "Hoxb7" "Irx1"
##
## $`positive regulation of leukocyte differentiation`
## [1] "Fos" "Bcl6" "Cd83" "Klf10" "Jun" "Irf1"
##
## $`positive regulation of hemopoiesis`
## [1] "Fos" "Bcl6" "Cd83" "Klf10" "Jun" "Irf1"
##
## $`regulation of myeloid leukocyte differentiation`
## [1] "Fos" "Klf10" "Jun" "Mafb" "Pik3r1"
##
## $`fibroblast proliferation`
## [1] "Ptprz1" "Jun" "Gstp1" "Anxa2" "Fth1"
##
## $`response to reactive oxygen species`
## [1] "Fos" "Rhob" "Lcn2" "Hspa8" "Jun" "Gstp1"
##
## $`protein glycosylation`
## [1] "B3gnt7" "Tmtc1" "Acer2" "Galnt3" "St3gal4" "Fut8"
##
## $`macromolecule glycosylation`
## [1] "B3gnt7" "Tmtc1" "Acer2" "Galnt3" "St3gal4" "Fut8"
##
## $`carboxylic acid transmembrane transport`
## [1] "Rgs2" "Slc6a7" "Arg2" "Slc16a11" "Lrrc8c"
##
## $`cellular response to epidermal growth factor stimulus`
## [1] "Fos" "Zfp36" "Gstp1"
##
## $`negative regulation of cell activation`
## [1] "Hspb1" "Bcl6" "Hfe" "Arg2" "Irf1" "Cx3cl1"
##
## $`fever generation`
## [1] "Ptgs2" "Ptges"
##
## $`membrane raft assembly`
## [1] "Cav2" "Anxa2"
##
## $`regulation of T-helper 2 cell differentiation`
## [1] "Bcl6" "Irf1"
##
## $`hepoxilin metabolic process`
## [1] "Gstp1" "Gstm1"
##
## $`hepoxilin biosynthetic process`
## [1] "Gstp1" "Gstm1"
##
## $`response to parathyroid hormone`
## [1] "Fos" "Cited1"
##
## $`positive regulation of glial cell migration`
## [1] "Ptprz1" "Cx3cl1"
##
## $`regulation of unsaturated fatty acid biosynthetic process`
## [1] "Ptgs2" "Pla2g4a"
##
## $`renal tubule morphogenesis`
## [1] "Bmp2" "Cited1" "Hoxb7" "Irx1"
##
## $`icosanoid metabolic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Gstp1" "Gstm1"
##
## $`positive regulation of intracellular transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Anxa2" "Pik3r1"
##
## $`regulation of intracellular transport`
## [1] "Ptgs2" "Chp2" "Sfn" "Hap1" "Ier3" "Anxa2" "Pik3r1"
##
## $`regulation of lipid transport`
## [1] "Ptges" "Lipg" "Pla2g4a" "Anxa2" "Ttc39b"
##
## $`monocarboxylic acid biosynthetic process`
## [1] "Ptgs2" "Ptges" "Lipg" "Pla2g4a" "Gstp1" "Gstm1"
##
## $`regulatory T cell differentiation`
## [1] "Hspb1" "Bcl6" "Irf1"
##
## $`unsaturated fatty acid metabolic process`
## [1] "Ptgs2" "Ptges" "Pla2g4a" "Gstp1" "Gstm1"
##
## $`organic acid transmembrane transport`
## [1] "Rgs2" "Slc6a7" "Arg2" "Slc16a11" "Lrrc8c"
##
## $`calcium ion transport`
## [1] "Ptgs2" "Mcub" "Tmem37" "Hap1" "Trpc1" "Cacna2d1" "Cx3cl1"
## [8] "Smim6" "Nos1"
##
## $`cellular response to reactive oxygen species`
## [1] "Fos" "Rhob" "Lcn2" "Hspa8" "Jun"
##
## $`positive regulation of prostaglandin secretion`
## [1] "Ptges" "Pla2g4a"
##
## $`regulation of odontogenesis of dentin-containing tooth`
## [1] "Bmp2" "Wnt10a"
##
## $`regulation of nuclear-transcribed mRNA poly(A) tail shortening`
## [1] "Btg2" "Zfp36"3.2 Downregulation Pathway
# Arrange and filter DEGs
df <- type_markers %>% arrange(desc(avg_log2FC))
df2 <- df %>% filter(p_val_adj < 0.05)
DEG_list <- df2
markers1down <- DEG_list %>% rownames_to_column(var="SYMBOL")
ENTREZ_list <- bitr(
geneID = rownames(DEG_list),
fromType = "SYMBOL",
toType = "ENTREZID",
OrgDb = org.Mm.eg.db
)## 'select()' returned 1:1 mapping between keys and columns## Warning in bitr(geneID = rownames(DEG_list), fromType = "SYMBOL", toType =
## "ENTREZID", : 3.19% of input gene IDs are fail to map...markers1down <- ENTREZ_list %>% inner_join(markers1down, by = "SYMBOL")
markers1down <- markers1down %>% dplyr::filter(p_val_adj < 0.05)
pos.markers1down <- markers1down %>% dplyr::filter(avg_log2FC < 0) %>% arrange(desc(abs(avg_log2FC)))
pos.ranks1down <- pos.markers1down$ENTREZID[abs(pos.markers1down$avg_log2FC) > 0.4]
# GO enrichment for downregulated genes
pos_go1down <- enrichGO(
gene = pos.ranks1down,
OrgDb = org.Mm.eg.db,
ont = "BP",
readable = TRUE
)
pos_go1down## #
## # over-representation test
## #
## #...@organism Mus musculus
## #...@ontology BP
## #...@keytype ENTREZID
## #...@gene chr [1:65] "268709" "54156" "18703" "15395" "12709" "192201" "27528" ...
## #...pvalues adjusted by 'BH' with cutoff <0.05
## #...22 enriched terms found
## 'data.frame': 22 obs. of 12 variables:
## $ ID : chr "GO:0070374" "GO:0042060" "GO:0022612" "GO:0032148" ...
## $ Description : chr "positive regulation of ERK1 and ERK2 cascade" "wound healing" "gland morphogenesis" "activation of protein kinase B activity" ...
## $ GeneRatio : chr "6/61" "7/61" "5/61" "3/61" ...
## $ BgRatio : chr "227/28928" "394/28928" "163/28928" "29/28928" ...
## $ RichFactor : num 0.0264 0.0178 0.0307 0.1034 0.0909 ...
## $ FoldEnrichment: num 12.53 8.43 14.55 49.06 43.11 ...
## $ zScore : num 8.02 6.82 7.97 11.9 11.13 ...
## $ pvalue : num 8.46e-06 1.91e-05 2.46e-05 3.13e-05 4.65e-05 ...
## $ p.adjust : num 0.0106 0.0106 0.0106 0.0106 0.0106 ...
## $ qvalue : num 0.00817 0.00817 0.00817 0.00817 0.00817 ...
## $ geneID : chr "Fgfbp3/Dusp15/Gas6/Egf/Fgf1/Notch2" "Plau/Plet1/Gas6/Cldn19/Fgf1/Notch2/Kng1" "Plau/Ntn1/Sostdc1/Fgf1/Notch2" "Gas6/Fgf1/Notch2" ...
## $ Count : int 6 7 5 3 3 3 3 6 6 3 ...
## #...Citation
## G Yu. Thirteen years of clusterProfiler. The Innovation. 2024, 5(6):100722# Visualization
chart1down <- dotplot(pos_go1down) +
ggtitle("type 1 downregulated control") +
theme_classic() +
theme(
plot.title = element_text(hjust = 0.5),
legend.position = "left",
axis.text.y = element_text(hjust = 0, size = 10)
) +
scale_y_discrete(
position = "right",
labels = function(x) str_wrap(x, width = 25)
)## Scale for y is already present.
## Adding another scale for y, which will replace the existing scale.
3.2.1 Downreg Gene View
pathway_type1down <- strsplit(pos_go1down$geneID, "/")
names(pathway_type1down) <- pos_go1down$Description
pathway_type1down## $`positive regulation of ERK1 and ERK2 cascade`
## [1] "Fgfbp3" "Dusp15" "Gas6" "Egf" "Fgf1" "Notch2"
##
## $`wound healing`
## [1] "Plau" "Plet1" "Gas6" "Cldn19" "Fgf1" "Notch2" "Kng1"
##
## $`gland morphogenesis`
## [1] "Plau" "Ntn1" "Sostdc1" "Fgf1" "Notch2"
##
## $`activation of protein kinase B activity`
## [1] "Gas6" "Fgf1" "Notch2"
##
## $`hepatocyte proliferation`
## [1] "Plau" "Fgf1" "Notch2"
##
## $`epithelial cell proliferation involved in liver morphogenesis`
## [1] "Plau" "Fgf1" "Notch2"
##
## $`liver morphogenesis`
## [1] "Plau" "Fgf1" "Notch2"
##
## $`regulation of ERK1 and ERK2 cascade`
## [1] "Fgfbp3" "Dusp15" "Gas6" "Egf" "Fgf1" "Notch2"
##
## $`regulation of cellular response to growth factor stimulus`
## [1] "Nrep" "Fgf9" "Fgfbp3" "Sostdc1" "Fgf1" "Notch2"
##
## $`renal absorption`
## [1] "Umod" "Gas6" "Cldn19"
##
## $`negative regulation of proteolysis`
## [1] "Ide" "Plau" "Timp3" "Gas6" "Kng1" "Anks1"
##
## $`ERK1 and ERK2 cascade`
## [1] "Fgfbp3" "Dusp15" "Gas6" "Egf" "Fgf1" "Notch2"
##
## $`regulation of epithelial cell proliferation`
## [1] "Plau" "Fgf9" "Egf" "Fmc1" "Fgf1" "Notch2"
##
## $`positive regulation of protein kinase activity`
## [1] "Vldlr" "Gas6" "Egf" "Fgf1" "Notch2"
##
## $`chaperone-mediated protein folding`
## [1] "Fkbp11" "Umod" "Pdcd5-ps"
##
## $`negative regulation of wound healing`
## [1] "Plau" "Cldn19" "Kng1"
##
## $`positive regulation of kinase activity`
## [1] "Vldlr" "Gas6" "Egf" "Fgf1" "Notch2"
##
## $`intracellular chloride ion homeostasis`
## [1] "Ckb" "Umod"
##
## $`vasculogenesis involved in coronary vascular morphogenesis`
## [1] "Fgf9" "Fgf1"
##
## $`activation of protein kinase activity`
## [1] "Gas6" "Fgf1" "Notch2"
##
## $`intracellular monoatomic anion homeostasis`
## [1] "Ckb" "Umod"
##
## $`fibroblast growth factor receptor signaling pathway`
## [1] "Fgf9" "Fgfbp3" "Fgf1"# Start filtering process here
# Maybe use genes you discover from Upset Plot
# Maybe try with subtypes fitler genes
gyarmati <- c("Fabp3", "Ccn1", "Foxq1", "Cxcl12", "Vash2", "Pamr1", "Vegfd", "Ccn3", "Bmp3", "Fgf9", "Spp1", "Wnt10a", "Sfrp1", "Tcf4", "Pappa2", "Unc5d", "Sema3c", "Robo2", "Slit2", "Egfl6", "Hgfac", "Pdgfc", "Megf9", "Frem1", "Thsd4", "Spock2", "Mmp14", "Adamtsl2", "Car8", "Irx1", "Irx2", "Hoxd11", "Hoxc4", "Etv1")
df3 <- type_markers %>%
filter(gene %in% gyarmati) %>%
arrange(desc(avg_log2FC))
df3 <- rownames(df3)
df <- AverageExpression(
object = SO4,
features = df3,
group.by = 'treatment'
)$RNA## As of Seurat v5, we recommend using AggregateExpression to perform pseudo-bulk analysis.
## Names of identity class contain underscores ('_'), replacing with dashes ('-')
## This message is displayed once per session.## 25 x 2 sparse Matrix of class "dgCMatrix"
## control low-salt
## Pappa2 6.591097e+35 1.304159e+66
## Frem1 6.673899e-01 3.198223e+00
## Wnt10a 2.273670e+00 7.980575e+00
## Robo2 6.943374e+15 1.199490e+20
## Hoxc4 8.302147e-01 1.078682e+00
## Irx1 5.138850e+16 3.271063e+20
## Megf9 1.427964e+02 6.102353e+03
## Irx2 2.409596e+10 5.795259e+09
## Etv1 2.207814e+01 6.491579e+01
## Bmp3 2.234102e+07 1.108405e+09
## Vegfd 3.172421e+00 5.166964e+00
## Sfrp1 8.596244e+87 3.679007e+88
## Vash2 3.939904e+00 3.543367e+01
## Spock2 8.860768e+01 8.436720e-01
## Hgfac 1.099643e+00 1.705886e+00
## Thsd4 3.184754e+02 1.560983e+02
## Adamtsl2 2.437454e+00 9.787557e+00
## Mmp14 2.911076e+00 4.862623e+00
## Hoxd11 2.703429e+00 4.963274e+00
## Pamr1 7.920054e+05 7.033070e+07
## Slit2 4.645370e+06 1.757724e+09
## Cxcl12 1.795344e+00 1.488615e+00
## Fgf9 7.375148e+04 4.247585e+06
## Fabp3 8.119897e+06 1.642683e+06
## Egfl6 1.330964e+01 3.049626e+00df <- as.data.frame(df)
df <- t(scale(t(df)))
# convert df to tidy format
# only use about 10-15 genes
df_tidy <- df %>%
as.data.frame() %>%
rownames_to_column(var = "Gene") %>%
pivot_longer(cols = -Gene, names_to = "treatment", values_to = "Expression")
# Graph with geom_tile
df_tidy$treatment <- factor(df_tidy$treatment, levels = c("control","low-salt"))
f4 <- ggplot(df_tidy, aes(x = treatment, y = Gene, fill = Expression)) +
geom_tile(color = "black", size = 0.2, width = 0.97, height = 0.90) + # Adds thin border and spacing between tiles
scale_fill_distiller(palette = "RdYlBu") +
theme_minimal() +
theme(
axis.text = element_text(size = 12, color = "black"),
axis.title = element_text(size = 14),
axis.ticks = element_blank(), # Removes tick marks
panel.grid = element_blank(), # Removes grid lines
legend.position = "bottom", # Centers the legend below the plot
legend.title = element_text(size = 14), # Increases legend title size
legend.text = element_text(size = 12) # Increases legend text size
) +
labs(x = "Cell Type", y = "Gene", fill = "Relative Expression")## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
df3 <- type_markers %>%
filter(gene %in% gyarmati) %>%
arrange(desc(avg_log2FC))
df3 <- rownames(df3)
df <- AverageExpression(
object = SO4,
features = df3,
group.by = 'sample'
)$RNA
df## 25 x 4 sparse Matrix of class "dgCMatrix"
## SO1 SO4 SO3 SO2
## Pappa2 1.631319e+27 9.502433e+35 4.599475e+50 4.357385e+66
## Frem1 5.051842e-01 7.390373e-01 2.467003e+00 4.910118e+00
## Wnt10a 4.987066e+00 1.075144e+00 9.814276e+00 3.687615e+00
## Robo2 2.266277e+16 3.841285e+08 2.292019e+13 4.007670e+20
## Hoxc4 1.163107e+00 6.831737e-01 1.048873e+00 1.148470e+00
## Irx1 6.022417e+13 7.406058e+16 2.529182e+17 1.092318e+21
## Megf9 1.206467e+02 1.525800e+02 7.966486e+03 1.738147e+03
## Irx2 5.855799e+10 8.873831e+09 1.028490e+09 1.695496e+10
## Etv1 3.699306e+00 3.019620e+01 2.293347e+01 1.632025e+02
## Bmp3 5.803240e+07 6.575880e+06 3.455761e+08 2.894297e+09
## Vegfd 2.114492e+00 3.639716e+00 4.471286e+00 6.795649e+00
## Sfrp1 2.805765e+88 3.457064e+78 5.250413e+88 1.161485e+84
## Vash2 2.151315e+00 4.729936e+00 8.024412e+00 9.960274e+01
## Spock2 2.857825e-01 1.276201e+02 8.631615e-01 7.980441e-01
## Hgfac 1.721668e+00 8.248896e-01 1.472557e+00 2.252142e+00
## Thsd4 3.658671e+01 4.429877e+02 1.772561e+02 1.065649e+02
## Adamtsl2 2.301601e+00 2.497462e+00 8.654869e+00 1.243935e+01
## Mmp14 2.742303e+00 2.985624e+00 4.180389e+00 6.459834e+00
## Hoxd11 4.322132e+00 1.988436e+00 4.259589e+00 6.610705e+00
## Pamr1 2.410947e+06 7.690718e+04 5.529267e+07 1.055369e+08
## Slit2 1.172151e+07 1.519789e+06 7.016234e+06 5.856385e+09
## Cxcl12 4.100233e+00 7.772582e-01 9.850546e-01 2.667524e+00
## Fgf9 2.161928e+04 9.677865e+04 4.320923e+04 1.409064e+07
## Fabp3 1.991354e+07 2.910558e+06 2.194586e+06 3.505956e+05
## Egfl6 1.428073e+01 1.288070e+01 1.542672e+00 6.577626e+00df <- as.data.frame(df)
df <- t(scale(t(df)))
# convert df to tidy format
df_tidy <- df %>%
as.data.frame() %>%
rownames_to_column(var = "Gene") %>%
pivot_longer(cols = -Gene, names_to = "sample", values_to = "Expression")
# Graph with geom_tile
df_tidy$sample <- factor(df_tidy$sample, levels = c("SO1","SO4","SO2","SO3"))
f4 <- ggplot(df_tidy, aes(x = sample, y = Gene, fill = Expression)) +
geom_tile(color = "black", size = 0.2, width = 0.97, height = 0.90) + # Adds thin border and spacing between tiles
scale_fill_distiller(palette = "RdYlBu") +
theme_minimal() +
theme(
axis.text = element_text(size = 12, color = "black"),
axis.title = element_text(size = 14),
axis.ticks = element_blank(), # Removes tick marks
panel.grid = element_blank(), # Removes grid lines
legend.position = "bottom", # Centers the legend below the plot
legend.title = element_text(size = 14), # Increases legend title size
legend.text = element_text(size = 12) # Increases legend text size
) +
labs(x = "Sample", y = "Gyarmati Genes", fill = "Relative Expression")
f4
4 Grouping as Treatment groups
# 1. Create new sample groups
treatmentgroup <- df_tidy %>%
mutate(
sample = case_when(
sample %in% c("SO1", "SO4") ~ "SO1_SO4",
sample %in% c("SO2", "SO3") ~ "SO2_SO3"
)
) %>%
# 2. Sum (or use mean) of Expression within each group for each Gene
group_by(Gene, sample) %>%
summarize(Expression = mean(Expression), .groups = "drop") # Use mean() if you prefer averaging
treatmentgroup$sample <- factor(treatmentgroup$sample, levels = c("SO1_SO4", "SO2_SO3"))
f4_grouped <- ggplot(treatmentgroup, aes(x = sample, y = Gene, fill = Expression)) +
geom_tile(color = "black", size = 0.2, width = 0.97, height = 0.90) +
scale_fill_distiller(palette = "RdYlBu") +
theme_minimal() +
theme(
axis.text = element_text(size = 12, color = "black"),
axis.title = element_text(size = 14),
axis.ticks = element_blank(),
panel.grid = element_blank(),
legend.position = "bottom",
legend.title = element_text(size = 14),
legend.text = element_text(size = 12)
) +
labs(x = "Control Low Salt ", y = "Gyarmati Genes", fill = "Relative Expression")
f4_grouped
# HeatMap of each clusters top genes from pathway analysis
